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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCTCTTTATTTGGAGCTGGGAAGAACCCGGCATGGCAGATGCTAGTTCGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctcttttctctgtcactctgtttatgctcctggtgattgatcatttatgcaagctaggtacaaaagccaaaacaacataggcactgtatctag...

Basic information

species Oryza sativa
transcript LOC_Os03g20310.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20310.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 2
TTGTCTCTTTATTTGGAGCTGGGAAGAACCCGGCATGGCAGATGCTAGTTCGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctcttttctctgtc-actctgt-ttatgctcctggtgattgatcatttatgcaagctaggtacaaaagccaaaacaacataggcactgtatctag
||||||| || || ||||||||  || || ||||||||||||||||||||||||||||||||| || || ||  | || |  || ||||||||||| | |||| |  ||||||||||  ||   | | | || || || |  ||||||||||||  ||  | ||        | |  |  | ||  | || |||||  || |
TTGTCTCATTCTTAGGAGCTGGCGAGCACTCGGCATGGCAGATGCTAGTTCGAGGACTGACACCTCGACTGTTGTAGACATGGATGATAAGAATCAAAGGgtagcccctcttttctccatctgttatatgttgtgttctttatgattgatcattcgtg--aactgttaggggatgatagcataatgttggtactgtgccttg

upper sequence: LOC_Os03g20310.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 3
TTGTCTCTTTATTTGGAGCTGGGAAGAACCCGGCATGGCAGATGCTAGTTCGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctcttttctctgtc------actctgt---ttatgctcctggtgattgatcatttatgcaagctaggtacaaaagccaaaacaacataggcactgtatctag
|||||||||| || ||||||||  || || ||||||||||||||||||||||||||||||||| || || ||  | || |  || ||||||||||| | |||| |  ||||||| ||  ||      |   | |   || || || |  |||||||||||   || |   | | ||    ||  || | ||||||     ||       
TTGTCTCTTTCTTAGGAGCTGGCGAGTACTCGGCATGGCAGATGCTAGTTCGAGGACTGACACCTCGACTGTTTTAGACATGGATGATAAGAATCAAAGGgtagcccctcttttttccatctgttgtatcttatatgttgtgttctttatgattgatcatccgtgaactgttgttaggggag--aagagaacataa-tgttga------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88407487|gb|CI586328.1|CI586328
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|218492876|gb|FG956101.1|FG956101
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|88345102|gb|CI628356.1|CI628356
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAG
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAG
EST: gi|88332679|gb|CI660197.1|CI660197
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAA
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAA
EST: gi|66916817|gb|CX103665.1|CX103665
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|58592490|gb|CF990798.1|CF990798
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|29658760|gb|CB655035.1|CB655035
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|5803454|gb|AI978424.1|AI978424
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|58591209|gb|CF989517.1|CF989517
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|88449999|gb|CI572130.1|CI572130
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTA
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTA
EST: gi|88432234|gb|CI565267.1|CI565267
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTTCATCTGATTGGTC
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATT-CATCTGATCGGTC
EST: gi|29658674|gb|CB654949.1|CB654949
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGATCGGTCT
EST: gi|88299315|gb|CI572267.1|CI572267
EST:     CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATG                         GTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGA
genomic: CGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctc ... atctttgcagGTAGACGGGCAAAGTGGAGCTATTGTGCCTTCTAATTCATCTGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCTCTTTATTTGGAGCTGGGAAGAACCCGGCATGGCAGATGCTAGTTCGAGGACTGACACATCAACAGTCCTGGATACCGACGATAAGAATCAGATGgtaacttctcttttctctgtcactctgtttatgctcctggtgattgatcatttatgcaagctaggtacaaaagccaaaacaacataggcactgtatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG